# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 16:42:41 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: N-[(benzyloxy)carbonyl]-L-alanyl-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)OCc1ccccc1)C(=O)N2CCC[C@H]2C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 ZAH  ZAH  N-[(benzyloxy)carbonyl]-L-alanyl-L-proline  ligand  42  23  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZAH
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 ZAH  C1    C  C      0   0.403   1.5942   0.5170  -4.5456
 ZAH  O2    O  O      0  -0.597   1.1843   1.6782  -4.3831
 ZAH  O20   O  OC    -1  -0.618   2.6855   0.1545  -5.0286
 ZAH  C3    C  CH1    0  -0.147   0.6223  -0.6284  -4.1966
 ZAH  C4    C  CH2    0  -0.493  -0.2443  -0.9886  -5.4145
 ZAH  C5    C  CH2    0  -0.459  -1.6053  -1.3325  -4.8204
 ZAH  C6    C  CH2    0  -0.286  -1.7254  -0.3409  -3.6733
 ZAH  N7    N  NT     0  -0.469  -0.3578  -0.2642  -3.1813
 ZAH  C8    C  C      0   0.568   0.0533   0.1286  -1.9760
 ZAH  O9    O  O      0  -0.515   1.2336   0.0918  -1.6396
 ZAH  C10   C  CH1    0  -0.199  -0.9997   0.6726  -1.0138
 ZAH  C11   C  CH3    0  -0.648  -1.3042   2.1319  -1.3565
 ZAH  N14   N  NH1    0  -0.662  -0.4889   0.5264   0.3268
 ZAH  C15   C  C      0   0.762  -1.2896   0.3666   1.3905
 ZAH  O16   O  O      0  -0.527  -2.5048   0.3391   1.3584
 ZAH  O17   O  O2     0  -0.482  -0.5713   0.2331   2.5130
 ZAH  C18   C  CH2    0  -0.238  -1.3000   0.0065   3.7247
 ZAH  C19   C  CR6    0   0.076  -0.2882  -0.1405   4.8203
 ZAH  C20   C  CR16   0  -0.294   0.0696   0.9492   5.6075
 ZAH  C21   C  CR16   0  -0.242   1.0241   0.8141   6.6074
 ZAH  C22   C  CR16   0  -0.262   1.6331  -0.4147   6.8250
 ZAH  C23   C  CR16   0  -0.242   1.2827  -1.5079   6.0420
 ZAH  C24   C  CR16   0  -0.287   0.3270  -1.3693   5.0457
 ZAH  H3    H  HCH1   0   0.234   1.1851  -1.5048  -3.8625
 ZAH  H4C1  H  HCH2   0   0.251   0.1897  -1.7998  -5.9972
 ZAH  H4C2  H  HCH2   0   0.235  -0.3461  -0.1257  -6.0777
 ZAH  H5C1  H  HCH2   0   0.237  -1.6106  -2.3526  -4.4304
 ZAH  H5C2  H  HCH2   0   0.249  -2.4224  -1.2397  -5.5348
 ZAH  H6C1  H  HCH2   0   0.255  -2.4163  -0.6790  -2.9023
 ZAH  H6C2  H  HCH2   0   0.237  -2.0686   0.6327  -4.0366
 ZAH  H10   H  HCH1   0   0.269  -1.9189   0.0900  -1.0875
 ZAH  H111  H  HCH3   0   0.235  -0.4036   2.7407  -1.2760
 ZAH  H112  H  HCH3   0   0.240  -1.6904   2.2360  -2.3701
 ZAH  H113  H  HCH3   0   0.245  -2.0531   2.5268  -0.6710
 ZAH  H14   H  HNH1   0   0.396   0.5136   0.5369   0.4434
 ZAH  H181  H  HCH2   0   0.247  -1.9721   0.8438   3.9241
 ZAH  H182  H  HCH2   0   0.246  -1.9035  -0.8989   3.6357
 ZAH  HA    H  HCR6   0   0.255  -0.4049   1.9097   5.4431
 ZAH  H21   H  HCR6   0   0.258   1.2908   1.6675   7.2173
 ZAH  H22   H  HCR6   0   0.259   2.3759  -0.5208   7.6052
 ZAH  H23   H  HCR6   0   0.258   1.7523  -2.4686   6.2094
 ZAH  H24   H  HCR6   0   0.255   0.0523  -2.2264   4.4414

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 ZAH  C1   O2    deloc     1.242  0.020  1.242
 ZAH  C1   O20   deloc     1.247  0.020  1.247
 ZAH  C1   C3    single    1.542  0.020  1.542
 ZAH  C3   C4    single    1.537  0.020  1.537
 ZAH  C3   N7    single    1.457  0.020  1.457
 ZAH  C3   H3    single    0.970  0.020  1.090
 ZAH  C4   C5    single    1.524  0.020  1.524
 ZAH  C4   H4C1  single    0.970  0.020  1.090
 ZAH  C4   H4C2  single    0.970  0.020  1.090
 ZAH  C5   C6    single    1.521  0.020  1.521
 ZAH  C5   H5C1  single    0.970  0.020  1.090
 ZAH  C5   H5C2  single    0.970  0.020  1.090
 ZAH  C6   N7    single    1.455  0.020  1.455
 ZAH  C6   H6C1  single    0.970  0.020  1.090
 ZAH  C6   H6C2  single    0.970  0.020  1.090
 ZAH  N7   C8    single    1.333  0.020  1.333
 ZAH  C8   O9    double    1.228  0.020  1.228
 ZAH  C8   C10   single    1.527  0.020  1.527
 ZAH  C10  C11   single    1.530  0.020  1.530
 ZAH  C10  N14   single    1.442  0.020  1.442
 ZAH  C10  H10   single    0.970  0.020  1.090
 ZAH  C11  H111  single    0.970  0.020  1.090
 ZAH  C11  H112  single    0.970  0.020  1.090
 ZAH  C11  H113  single    0.970  0.020  1.090
 ZAH  N14  C15   single    1.341  0.020  1.341
 ZAH  N14  H14   single    0.860  0.020  1.020
 ZAH  C15  O16   double    1.216  0.020  1.216
 ZAH  C15  O17   single    1.339  0.020  1.339
 ZAH  O17  C18   single    1.432  0.020  1.432
 ZAH  C18  C19   single    1.499  0.020  1.499
 ZAH  C18  H181  single    0.970  0.020  1.090
 ZAH  C18  H182  single    0.970  0.020  1.090
 ZAH  C19  C20   aromatic  1.391  0.020  1.391
 ZAH  C19  C24   aromatic  1.393  0.020  1.393
 ZAH  C20  C21   aromatic  1.389  0.020  1.389
 ZAH  C20  HA    single    0.930  0.020  1.080
 ZAH  C21  C22   aromatic  1.389  0.020  1.389
 ZAH  C21  H21   single    0.930  0.020  1.080
 ZAH  C22  C23   aromatic  1.390  0.020  1.390
 ZAH  C22  H22   single    0.930  0.020  1.080
 ZAH  C23  C24   aromatic  1.388  0.020  1.388
 ZAH  C23  H23   single    0.930  0.020  1.080
 ZAH  C24  H24   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 ZAH  C3    C1   O20   115.03  3.000
 ZAH  C3    C1   O2    117.18  3.000
 ZAH  O20   C1   O2    127.67  3.000
 ZAH  H3    C3   N7    109.48  3.000
 ZAH  H3    C3   C4    110.14  3.000
 ZAH  N7    C3   C4    103.38  3.000
 ZAH  H3    C3   C1    109.88  3.000
 ZAH  N7    C3   C1    113.31  3.000
 ZAH  C4    C3   C1    110.48  3.000
 ZAH  H4C2  C4   H4C1  107.49  3.000
 ZAH  H4C2  C4   C5    109.36  3.000
 ZAH  H4C1  C4   C5    113.35  3.000
 ZAH  H4C2  C4   C3    110.37  3.000
 ZAH  H4C1  C4   C3    111.95  3.000
 ZAH  C5    C4   C3    104.32  3.000
 ZAH  H5C2  C5   H5C1  108.06  3.000
 ZAH  H5C2  C5   C6    112.32  3.000
 ZAH  H5C1  C5   C6    109.83  3.000
 ZAH  H5C2  C5   C4    113.26  3.000
 ZAH  H5C1  C5   C4    110.75  3.000
 ZAH  C6    C5   C4    102.56  3.000
 ZAH  H6C2  C6   H6C1  108.20  3.000
 ZAH  H6C2  C6   N7    111.10  3.000
 ZAH  H6C1  C6   N7    111.91  3.000
 ZAH  H6C2  C6   C5    110.76  3.000
 ZAH  H6C1  C6   C5    112.43  3.000
 ZAH  N7    C6   C5    102.42  3.000
 ZAH  C8    N7   C6    127.67  3.000
 ZAH  C8    N7   C3    119.76  3.000
 ZAH  C6    N7   C3    112.53  3.000
 ZAH  C10   C8   O9    120.07  3.000
 ZAH  C10   C8   N7    117.54  3.000
 ZAH  O9    C8   N7    122.38  3.000
 ZAH  H10   C10  N14   107.89  3.000
 ZAH  H10   C10  C11   109.07  3.000
 ZAH  N14   C10  C11   112.06  3.000
 ZAH  H10   C10  C8    110.38  3.000
 ZAH  N14   C10  C8    107.79  3.000
 ZAH  C11   C10  C8    109.64  3.000
 ZAH  H113  C11  H112  107.88  3.000
 ZAH  H113  C11  H111  108.61  3.000
 ZAH  H112  C11  H111  107.95  3.000
 ZAH  H113  C11  C10   109.98  3.000
 ZAH  H112  C11  C10   111.72  3.000
 ZAH  H111  C11  C10   110.60  3.000
 ZAH  H14   N14  C15   120.18  3.000
 ZAH  H14   N14  C10   117.26  3.000
 ZAH  C15   N14  C10   122.55  3.000
 ZAH  O17   C15  O16   123.77  3.000
 ZAH  O17   C15  N14   110.89  3.000
 ZAH  O16   C15  N14   125.34  3.000
 ZAH  C18   O17  C15   116.87  3.000
 ZAH  H182  C18  H181  108.09  3.000
 ZAH  H182  C18  C19   110.58  3.000
 ZAH  H181  C18  C19   110.93  3.000
 ZAH  H182  C18  O17   110.10  3.000
 ZAH  H181  C18  O17   110.27  3.000
 ZAH  C19   C18  O17   106.89  3.000
 ZAH  C24   C19  C20   119.08  3.000
 ZAH  C24   C19  C18   120.21  3.000
 ZAH  C20   C19  C18   120.70  3.000
 ZAH  HA    C20  C21   119.76  3.000
 ZAH  HA    C20  C19   119.72  3.000
 ZAH  C21   C20  C19   120.52  3.000
 ZAH  H21   C21  C22   120.09  3.000
 ZAH  H21   C21  C20   119.89  3.000
 ZAH  C22   C21  C20   120.02  3.000
 ZAH  H22   C22  C23   120.13  3.000
 ZAH  H22   C22  C21   120.05  3.000
 ZAH  C23   C22  C21   119.82  3.000
 ZAH  H23   C23  C24   119.90  3.000
 ZAH  H23   C23  C22   120.11  3.000
 ZAH  C24   C23  C22   119.98  3.000
 ZAH  H24   C24  C23   119.73  3.000
 ZAH  H24   C24  C19   119.70  3.000
 ZAH  C23   C24  C19   120.57  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 ZAH  CONST_01  C22  C21  C20  C19    0.00   0.0  0
 ZAH  CONST_02  C22  C23  C24  C19    0.00   0.0  0
 ZAH  CONST_03  C23  C24  C19  C20    0.00   0.0  0
 ZAH  CONST_04  C23  C22  C21  C20    0.00   0.0  0
 ZAH  CONST_05  C24  C19  C20  C21    0.00   0.0  0
 ZAH  CONST_06  C24  C23  C22  C21    0.00   0.0  0
 ZAH  CONST_07  C21  C20  C19  C18  180.00   0.0  0
 ZAH  CONST_08  C23  C24  C19  C18  180.00   0.0  0
 ZAH  CONST_09  H21  C21  C20  C19  180.00   0.0  0
 ZAH  CONST_10  H23  C23  C24  C19  180.00   0.0  0
 ZAH  CONST_11  H24  C24  C19  C20  180.00   0.0  0
 ZAH  CONST_12  H22  C22  C21  C20  180.00   0.0  0
 ZAH  CONST_13  HA   C20  C21  C22  180.00   0.0  0
 ZAH  CONST_14  O9   C8   N7   C3     0.00   0.0  0
 ZAH  CONST_15  C10  C8   N7   C3   180.00   0.0  0
 ZAH  CONST_16  O9   C8   N7   C6   180.00   0.0  0
 ZAH  CONST_17  C10  C8   N7   C6     0.00   0.0  0
 ZAH  Var_01    C6   C5   C4   C3    36.59  30.0  1
 ZAH  Var_02    C5   C6   N7   C3    24.03  30.0  1
 ZAH  Var_03    N7   C6   C5   C4   -36.54  30.0  1
 ZAH  Var_04    C20  C19  C18  O17   95.27  30.0  2
 ZAH  Var_05    C19  C18  O17  C15  178.67  30.0  3
 ZAH  Var_06    O16  C15  N14  C10   -0.73  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 ZAH  chir_01  C3   C1   C4  N7   positiv
 ZAH  chir_02  C10  N14  C8  C11  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 ZAH  plan-1  C18  0.020
 ZAH  plan-1  C19  0.020
 ZAH  plan-1  C20  0.020
 ZAH  plan-1  C21  0.020
 ZAH  plan-1  C22  0.020
 ZAH  plan-1  C23  0.020
 ZAH  plan-1  C24  0.020
 ZAH  plan-1  HA   0.020
 ZAH  plan-1  H21  0.020
 ZAH  plan-1  H22  0.020
 ZAH  plan-1  H23  0.020
 ZAH  plan-1  H24  0.020
 ZAH  plan-2  C3   0.020
 ZAH  plan-2  C6   0.020
 ZAH  plan-2  N7   0.020
 ZAH  plan-2  C8   0.020
 ZAH  plan-2  O9   0.020
 ZAH  plan-2  C10  0.020
 ZAH  plan-3  C1   0.020
 ZAH  plan-3  O2   0.020
 ZAH  plan-3  O20  0.020
 ZAH  plan-3  C3   0.020
 ZAH  plan-4  N14  0.020
 ZAH  plan-4  C15  0.020
 ZAH  plan-4  O16  0.020
 ZAH  plan-4  O17  0.020

